Journal of Genetic Resources
Volume:7 Issue: 2, Summer-Autumn 2021

Capparis spinosa grows naturally from the Atlantic coast of the Canary Islands and Morocco to the Black Sea, in Crimea and Armenia, and to the east side of the Caspian Sea in Iran. Capparis species are valuable as a resource for medicine, food, improving soil fertility, stabilizing dunes, fuel, timber, and livestock feed. In this research, sixteen populations of Capparis spinosa were collected from different locations in Iran and quantitative and qualitative data of morphological characters were revised. A multivariable statistical analysis was performed for the morphological characters of Capparis populations. The populations were classified into two main groups using a Ward'shierarchicalclustering method. We showed some of the climatic conditions correlate with morphological characters. Data obtained were standardized (Mean= 0, variance= 1) and used to estimate Euclidean distance for clustering and ordination analyses. PCA (Principal components analysis) was used to identify the most variable morphological characters among the studied populations. The Redundancy Analysis (RDA) was applied to the dataset of nine explanatory environmental variables (annual precipitation and temperature, number of frost days, relative humidity, potential evapotranspiration, minimum and maximum absolute temperatures, minimum temperature of the coldest month of the year, and maximum temperature of the warmest month). In the Flora of Iran and Flora Iranica C. spinosa and C. sicula are considered as synonyms, which are improved by this study.

Cantharellus is one of the most widely used ectomycorrhizal fungus in the world, which forms mycorrhizal communities with various plant species and plays a major ecological role in forest ecosystems. The present study is the first report to know the extent of genetic diversity and differentiation of Zarde-Kija mushroom populations using microsatellite markers within the internal transcribed spacer (ITS). In this study, 70 fungal samples were collected from six populations of this species in the Hyrcanian Forest (Gorgan, Neka, Sari, Noor, Chalous, and Rasht populations) and its genetic diversity and structure were measured. The number of observed alleles ranged from 5 to 7 and the expected heterozygosity ranged from 0.320 to 0.864. AMOVA analysis showed that the largest portion of the genetic variation was among individuals within the population (95%), whereas 5% was among populations. The mean coefficient of differentiation (FST) was 0.096, which indicates the medium genetic differentiation between the populations under study. The mean inbreeding value (FIS) and gene flow (NM) were 0.853, 2.509, respectively. Most loci showed deviation from Hardy–Weinberg equilibrium due to the excess of heterozygotes in all populations. The genetic landscape shape plot revealed that high pairwise genetic distances among individuals in central populations of the Hyrcanian forest. This study revealed that the effective population size of Zarde-Kija has been decreased in the Hyrcanian forest and emphasizes the need to develop an effective strategy for the conservation of this species. However, it is suggested that research on this species be repeated using stronger markers and more populations to increase the accuracy of the results.

The late Embryogenesis Abundant (LEA) protein family obtains a group of stress-induced hyper-hydrophilic proteins that accumulate in response to cellular dehydration. They are generally unstructured polypeptides without a well-defined three-dimensional structure and have been identified in a wide range of organisms from bacteria to higher plants. Herein, we made a phylogenetic and evolutionary analysis for LEA proteins in Poaceae. The full-length LEA protein sequences were acquired by performing the sequence search of sequenced hva1 against Poaceae species in the non-redundant protein database by a BlastX search tool. The sequences were aligned with the Clustal Omega tool. The MEME suite searched for conserved blocks among each LEA protein sequence. Also, the evolutionary relationship among the LEA protein sequences evaluates using the MEGA tool. The results display close sequence similarity not only into the species but also between species. The results demonstrated that LEA proteins cluster into two large subgroups. The overall average evolutionary difference in LEA protein sequence pairs estimated as 0.4022 amino acid substitutions per site from averaging over all sequence pairs. The LEA protein sequences contain a significant percentage of glycine residues but lack cysteine and tryptophan residues. The results indicate the occurrence of homologs in the subgroup before the divergence of the species. However, the expansion of the gene number in the Poaceae was approved by the duplication events in the preexisting genes rather than by the appearance of the altered LEA gene. Our data will provide novel insights for further studies of the Late Embryogenesis Abundant protein family in Poaceae.

Lipases are particularly important because they specifically hydrolyze acyl glycerol, oils, which are of great interest for different industrial applications. Some halophilic microorganisms produced some lipases. Halophilic bacteria have greater ability to produce salt and thermo tolerant enzymes like amylases, proteases and lipases. Most industrial enzymatic functions may be stopped by concentrated salt solutions and high temperatures; therefore, halophilic enzymes that have optimal activity at a vast range of temperature, pH and ionic strength, would be considered as suitable biocatalysts in industrial processes. The aim of this study was to isolate and study the halophilic lipase producing bacteria from the Miankaleh Wetland. The lipase activity was measured using titrimetric methods. Three halophilic strains (AR11, AR18 and AR28) were isolated from the Miankaleh wetland and were screened for the production of hydrolytic enzymes and lipolytic activity. Among three isolates, one strain was selected for identification using the molecular methods and some morphological characteristics. The bacterium Halobacillus truperi AR11 with 1.82 ± 0.1 U/mL lipase activity was selected as the highest lipase producing isolate. Lipase enzyme produced by this potential isolate was also characterized for determining its optimal activity. Effect of different pH, NaCl concentration and temperature on lipase activity was determined. The optimum pH for AR11 was found to be 9, while the optimum temperature and NaCl concentration for lipase activity was found to be 45ºC and 5 % NaCl, respectively. This is the first report of isolation and molecular identification of lipase producing halophilic bacteria from the Miankaleh wetland.

Western forests of Iran are considered the richest biological resources of Iran. The rangelands of forest provide the bulk of the forage needed for livestock of nomads and villagers in the region. Therefore, research on this forest vegetation is very necessary. In this research, the studied area is part of the middle-sized Zagros forest ecosystem located in the Kaseh-Garan of Gilan-e-Gharb area (Kermanshah province, Iran). This research aims to achieve the effect of the canopy cover of bean trefoil (Anagyris foetida) as a nursing plant in identifying accompanying species and also identifying the dominant flora of the region. For this purpose, 55 samples were taken based on a randomized pattern with 100 * 100 m network dimensions. By inserting 1 × 1 m microplates into each plot, the total number of plants per unit area was investigated. The results of land surveying in the forests of the region showed that A. foetida with 61.5% had the highest coverage. Also, all of the plant specimens of this area were collected and identified using botanical resources in the Razi University herbarium (RUHK). In the floristic study, a total number of 333 plant species were belonging to 225 genera and 58 families. Among the plant families, Asteraceae had the highest number of plant species with about 19%. In terms of life forms, the highest percentage for both therophytes and hemicritophytes (41%) were found. In the chorological study, the highest frequency related to the Irano-Turanian elements (66%), Irano-Turanian, and Mediterranean areas (9%), Irano-Turanian, the Mediterranean, and Euro-Siberian (8%), Irano-Turanian and Euro-Siberian (7%), and remaining 10 percent related to species with other geographical distribution in the area. Although the Kaseh-Garan area is phytogeographically related to Irano-Turanian, elements from the Mediterranean and Sahara-Sindian have infiltrated this region. Therefore, the presence of bean trefoil stands (with 61.5% coverage), high floristic diversity, and special vegetation of Kaseh-Garan shows the importance of this region and the protection of vegetation in this area is necessary.

Chromosomal aneuploidies are the most chromosomal abnormalities at birth due to maternal meiosis I errors. Pregnancies with autosomal chromosomal aneuploidies that survive are namely trisomies 13 (Patau syndrome), 18 (Edward syndrome), and 21 (Down syndrome), account for 89% of chromosome abnormalities. Quantitative fluorescent polymerase chain reaction (QF-PCR) which amplifies specific DNA sequences called short tandem repeats (STRs), by using fluorescently labeled primers is a rapid technique for prenatal diagnosis of common aneuploidies. In this study, DNA extraction was performed from 100 samples isolated from muscle tissue of aborted fetuses. The analysis was performed by multiplex QF-PCR using a panel of 25 STRs markers for chromosomes X, Y, 13, 18, and 21. Our results showed that 20% of abortions were due to aneuploidy. 53% of mothers who had abortions were aged 26-35 years old and 32% of them were aged 36-45 years old. The analysis of muscle samples of aborted fetuses indicated that 20 samples showed chromosomal aneuploidy. Of the abnormal cases, 10 cases (~50 %) showed trisomy 21 followed by trisomy 18 (7 cases, ~35%), Klinefelter syndrome (2 cases, ~10 %), and showed trisomy X (1 case, ~5 %). Our results indicated that the D21S1414 marker showed the highest rate of heterozygosity in the study population. Besides some limitations of this study such as sample size, these results suggest that one of the causes of these abortions could be maternal age. We concluded that QF-PCR could be a rapid and reliable method to screen prenatal chromosomal aneuploidy and allow appropriate counseling.

Lettuce mosaic virus (LMV) is one of the most important and destructive members of Potyviruses in the family Potyviridae that is transmitted by aphid and seed which cause economic damage and serious yield losses to different crops around the world. To explore phylogenetic relationships, population evolution, and the effect of selection forces on the complete coat protein (CP) gene of LMV isolates, 36 complete coat protein gene sequences retrieved from the GenBank database in several different countries in four continents: Central and East Asia (China, Taiwan, South Korea, and Turkey), Europe (France), Africa (Tunisia), and America (Chile and Brazil). The phylogenetic tree of LMV isolates was grouped into independent clades with the significance of FST values (>0.27). The ratio of dN/dS is calculated less than one and showed that the LMV-CP has been under negative selection. Statistical tests (Tajima’s D, Fu and Li’s D* and F*) were used to estimate non-significantly negative values for all clades and geographic populations except for the Brazilian population and Clade III in a phylogenetic group. The negatives values revealed that there is less polymorphism estimation. All geographic populations in four phylogroups of LMV seem to be at equilibrium because all neutrality test statistics were non-significant. The findings suggested that the dynamics of LMV molecular evolution may be dependent on mutation, recombination, and negative selection. No recombination events were observed in this part of the LMV genome. Therefore, this study provides the first time evolution and differentiation between populations of LMV isolates from around the world and suggested that they may be occurred by the transmission of the virus among lettuce plants by types of aphid species, migration in different geographical areas by infected seeds and plant material, and broad host range which seems that these events have played an important role in shaping the LMV population structure.

The absence of recombination, high rate of mutation, and maternal inheritance of the mitochondrial DNA (mtDNA) genome makes it a valuable tool in many fields including evolutionary anthropology, genetic genealogy, population history, and forensic science. The mtDNA genome can be separated into two parts: a large coding region and a smaller fragment called the control region or non-coding region that generally referred to as displacement loop (D loop). The mtDNA D-loop region was highly polymorphic and has proven a precious marker in forensic identification. The study aims to examine and suggests polymorphism of the HVRIII region as a power marker along with HVRI and HVRII in forensic investigations. Within the control region of the mtDNA genome, the sequences of hypervariable region III (HVR III) (nucleotide position 438-574) were obtained from 60 unrelated Muslims of Shrirangapattana town, located in Karnataka state of South India. The complete mtDNA control region was amplified and sequenced by the Sanger sequencing method. The study provided the identification of 18 different haplotypes and 17 polymorphic nucleotide positions. The most common haplotype (H.18) was consistent with the Anderson sequence which occurred fourteen times. The distribution of nucleotide substitutions, insertions, and deletions was computed and determined that transitions made up the majority of the variations (58%) in this region. The genetic diversity was estimated at 0.89939 and the random match probability at 0.1155. The power of discrimination was found to be 0.8844 and the rest of the statistical parameters such as the mean of pair-wise differences and nucleotide diversity were established as 2.255932 ± 1.25884 and 0.010071± 0.00623, respectively. Consequently, the discovery of high genetic, haplotype, and nucleotide diversity, and high power of discrimination impart the use of hypervariable region III (HVR III) as an important marker in forensic investigations.

Single Nucleotide Polymorphisms, especially non-synonymous single-nucleotide polymorphisms (nsSNPs), which are the cause of various diseases, are a major issue in genetics. NsSNPs in protein-coding genes can cause functional and structural variations in the altered protein. The human CXCL10 gene, localized on chromosome 4q21, is a pro-inflammatory cytokine and plays a role in diverse and critical biological mechanisms. Despite its significance, there is not any document about the impact of variations mapped to this protein. Accordingly, we gathered data about SNPs on the CXCL10 protein and examined the diverse effects of deleterious ones on the function and structure of the protein using various web-based tools. Our analyses indicated that 9 most deleterious nsSNPs (identified by SIFT, PROVEAN, PolyPhen-2, SNPs&GO, PhD-SNP, SNAP2, and PMut) in the conserved region of the CXCL10 affect the molecular function and stability of the protein. By utilizing RMSD values, we concluded that these substitutions in the native structure cause several changes in the protein, including in the N-terminal end, which is vital for binding to the receptor, and finally results in altered regulation, expression, function, and consequently leads to different diseases. Furthermore, some SNPs on the 3′ UTR site showed pattern alterations in the upstream open reading frames (uORFs) and BRD-BOX; moreover, SNPs in this area result in significant changes in miRNA binding sites consequently. Finally, by some analyses, we identified that the CXCL10 deregulation might be a proper prognostic marker in gastric and ovarian cancer. These types of studies help scientists determine whether SNPs are worth following for additional experimental studies to maximize the outcome while studying human health.

The exposure of seeds to undesirable soil conditions induces secondary dormancy and this causes many problems for seed producers. Assessing seed secondary dormancy potential is an important factor in developing rapeseed lines and cultivars. A relatively rapid, precise, and reproducible method derived from the Hohenheim standard dormancy test (HSDT) has been developed for secondary dormancy evaluation of 41 rapeseeds (Brassica napus L.) lines and 5 cultivars. The two previous methods, HSDT and rapid secondary dormancy (RDT) were compared with our suggested fast-reproducible dormancy test (FRDT) method. All three methods consider three stages for seeds i.e. dormancy induction, germination in darkness, and breaking secondary dormancy. In the FRDT method, time to germination in darkness and seed dormancy breakage duration decreased to 7 and 4 days, respectively, whereas the corresponding figures in the HSDT were 14 and 7 days. Meanwhile, the duration of the three stages in sum decreased from 35 to 25 days. The obtained ranges of seed dormancy in different lines and cultivars as assessed by HSDT, FRDT, and RDT varied from 6 to 98.75, 7.5 to 99, and 0 to 36%, respectively. Positive relationships were found between data of the seed secondary dormancy testing by HSDT and FRDT methods. Owe to the precise and reproducible estimates, both HSDT and FRDT methods can be used for testing seed secondary dormancy in different rapeseed lines and cultivars. This method helps seed breeders to improve the screening of new rapeseed lines and cultivars with lower potential for secondary dormancy and as a result reduce the risk of volunteer rapeseed emergence in the field, which compromises yield in the next growing season.

The current research was conducted to study the effects of different fatty acids sources in the diet on blood metabolites and hormones in finishing lambs experimentally infected with the virus that causes foot and mouth disease. A total of fifteen Sangsari male lambs with an average live weight of 48±2 kg and an average age of 8±1 month were randomly assigned to one of three dietary experimental treatments as follows: 1) Calcium soap of palm oil fatty acids (PO) as a source of palmitic acid (16:0); 2) Calcium soap of sunflower oil fatty acids (SO) as the source of linoleic acid (n-6 18:2); and 3) Calcium soap of linseed oil fatty acids (LO) as the source of α-linolenic acid (n-3 18:3). The lambs were housed in individual pens and offered the iso-caloric and iso-nitrogenous diets for 28 days including 21 days of adaptation period and 7 days of the sampling period. The results illustrated that the lowest and the highest expression of IL-4 mRNA were measured in LO and SO treatments, respectively. Expression of IL-8 mRNA was lower in LO and PO treatments when compared with SO. The highest level of glucose in LO treatment when compared with sunflower oil or palm oil. Lambs on the LO diet showed the highest blood concentration of insulin and the lowest blood concentration of glucagon when compared with lams on SO and PO diets. The highest blood contents of triiodothyronine and thyroxin hormones were measured in lambs on the LO diet when compared with other treatments. However, the concentration of blood glucose, insulin, glucagon, triiodothyronine, and thyroxin were the same between PO and SO groups. In conclusion, the findings of the current experiment confirmed that the inclusion of α-linolenic acid but not linoleic acid in the diet of virus-infected lambs suppressed pro-inflammation with lowering expression of IL-4 and IL-8 mRNA and increased blood glucose, insulin, T3, and T4 which may lead to higher weight gain and feed efficiency of virally infected lambs.

Lead, cadmium, and copper are common environmental pollutants in most industrialized countries. Soil with heavy metal pollution has raised concern in recent years due to its possible destructive effects on plants system. In the present investigation, we studied the genotoxic effect of lead, cadmium, and copper on mitotic chromosomes of Trigonella foenum-graecum L. for the first time. The root tips of T. foenum-graecum were treated with four graded concentrations (viz. 50, 100, 150, and 200 ppm) of lead, cadmium, and copper. After hydrolyzing the root end in hydrochloric acid solution, they were stained with acetocarmine. After squashing the root end, they were studied under a microscope. To this end, the mitotic index (MI) and the total percentage of abnormality (TAP%) were analyzed. Studying of the root end of T. foenum-graecum showed that this plant is diploid and its chromosomal base number is 2x=2n=16. Cytological monitoring revealed that Pd, Cd, and Cu exhibit mitodepressive behaviors at higher concentrations. Moreover, the mitotic index decreases, but the incidence of different anomalies, such as sticky chromosome, c-mitosis, micronucleus, laggard chromosome, bridge, and precocious movement, increase through increasing heavy metal concentration. Among the mitotic abnormalities observed in all treatments, the highest percentage was related to the sticky chromosome. The highest genotoxic potential was observed in the lead, followed by cadmium and copper. The results showed that heavy metal pollution led to a significant MI reduction and TAP% increase in root tip meristems of T. foenum-graecum. This should be considered as a risk warning of the environmental pollution on plants, especially medicinal plants.